[med-svn] [tantan] 09/14: Merge tag 'upstream/13'

[Sascha Steinbiss]

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sascha-guest pushed a commit to branch master
in repository tantan.

commit 8be446275383fdc5fbe27eb273f05084eb8b7a6a
Merge: bb07b96 2fac365
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Thu Feb 11 09:45:34 2016 +0000

    Merge tag 'upstream/13'
    
    Upstream version 13

 COPYING.txt                     |  674 ++++++++++++++++++
 ChangeLog.txt                   |   84 +++
 Makefile                        |   25 +
 README.html                     |  523 ++++++++++++++
 README.txt                      |  187 +++++
 debian/changelog                |    7 -
 debian/compat                   |    1 -
 debian/control                  |   20 -
 debian/copyright                |   31 -
 debian/createmanpages           |   16 -
 debian/lintian-overrides        |    1 -
 debian/manpages                 |    1 -
 debian/rules                    |   16 -
 debian/source/format            |    1 -
 debian/tantan.1                 |   58 --
 debian/upstream/edam            |   13 -
 debian/upstream/metadata        |   11 -
 debian/watch                    |    2 -
 src/CA_code/lambda_calculator.c |  465 ++++++++++++
 src/CA_code/lambda_calculator.h |   10 +
 src/CA_code/lubksb.c            |   24 +
 src/CA_code/ludcmp.c            |   61 ++
 src/CA_code/nrutil.c            |  239 +++++++
 src/CA_code/nrutil.h            |   19 +
 src/Makefile                    |   27 +
 src/mcf_alphabet.cc             |   82 +++
 src/mcf_alphabet.hh             |   52 ++
 src/mcf_fasta_sequence.cc       |  113 +++
 src/mcf_fasta_sequence.hh       |   29 +
 src/mcf_score_matrix.cc         |  167 +++++
 src/mcf_score_matrix.hh         |   60 ++
 src/mcf_score_matrix_probs.cc   |   45 ++
 src/mcf_score_matrix_probs.hh   |   55 ++
 src/mcf_tantan_options.cc       |  165 +++++
 src/mcf_tantan_options.hh       |   31 +
 src/mcf_util.cc                 |   23 +
 src/mcf_util.hh                 |   46 ++
 src/tantan.cc                   |  462 ++++++++++++
 src/tantan.hh                   |  120 ++++
 src/tantan_app.cc               |  293 ++++++++
 src/version.hh                  |    1 +
 test/atMask.mat                 |   14 +
 test/hg19_chrM.fa               |  333 +++++++++
 test/panda.fastq                |  400 +++++++++++
 test/tantan_test.out            | 1489 +++++++++++++++++++++++++++++++++++++++
 test/tantan_test.sh             |   31 +
 test/titin_human.fa             |  688 ++++++++++++++++++
 47 files changed, 7037 insertions(+), 178 deletions(-)

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